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Interfacial physics of field-effect biosensors
No full textField-Effect Transistor-sensors (FET-sensors) are a class of pH and biomolecule sensors that can be produced at a low cost and with high sensitivity, as a result having potential for commercialisation and widespread use. The response of a FET-sensor is generated when the electric field at the sensor surface changes, thereby inducing a measurable change in current through the device. The electric field can be modified by pH or by binding of an analyte to the surface. The solid state counterpart, the Metal Oxide Semiconductor FET, has been extensively studied as it is the basis of modern electronics. FET-sensors are less well understood, mainly due to the inherent complexity introduced by the aqueous media present at the sensor surface. The FET-sensor surface is usually an oxide such as silica and its interaction with aqueous solution introduces many complex effects, such as ion-dynamics and pH dependent ionisation, which make these systems non-trivial to understand and predict. To-date, most models of FET-sensor response have relied upon mean-field assumptions which neglect the multi-scale nature of the system and even qualitative predictions of FET-sensor response remain challenging.In the work presented here, the interfacial physics of FET-sensors were modelled using a variety of simulation techniques at different time- and length-scales. Acid-base surface charging reactions at the oxide surface of the sensor are an important part of FET-sensor response. Density Functional Theory (DFT) simulations revealed a new mechanism of surface charging and also showed that these reactions have no well-defined transition state which can be used to model their kinetics. A Kinetic Monte Carlo (KMC) model was validated that can be used describe the dynamics of surface-charging reactions on a device scale.As FET-sensors operate by detecting changes in the interfacial electric field, the mean net charge density of surface-bound biomolecules is an important parameter in most models of BioFET response. Semi-empirical calculations were performed to estimate the net charge of two different biomolecular systems relevant to biosensing studies. The ion dynamics in the electrical double layer at the silicawater-biomolecule interface were investigated using classical Molecular Dynamics (MD) simulations, which suggested that, in contrast to commonly used net-charge arguments for FET-sensor response, the importance of water polarisation for FET-sensor response has been hitherto underestimated.A quantitative analysis of data extracted from the FET-sensor literature was performed, comparing experimental biosensing data with pH-sensing data. This revealed some frequent problems related to reproducibility and comparability of experimental data in this field, and highlighted that optimisation of surface chemistry is an underappreciated component of sensor optimisation. Despite these limitations, BioFET research is a rapidly advancing field in which novel device design and operation methodologies are constantly being developed which increase the viability of BioFET devices for commercial use
Supplementary Data for Paper Entitled "Acid-base dissociation mechanisms and energetics at the silica–water interface: an activationless process"
No full textPublication Submission Contents includes the publication (lyx document) and images in respective subfolders.
XYZ animations includes .xyz file-format trajectories showing the geometry optimisations from the paper
Raw Data archive provides raw data used in simulations (input files and output files <5Mb)</span
Dataset for "Interfacial Physics of Field-Effect Biosensors"
No full textSupporting Data for:
Lowe, Benjamin (2016). Interfacial Physics of Field-Effect Biosensors. University of Southampton, Doctoral Thesis.
See attached README.txt for more details and acknowledgements.
The results of the thesis begin from Chapter 4 onwards and data is included for each Chapter as described below:
Chapter 4: Charging at the Silica-Water Interface.
In the folder "silica_water_DFT" are the results of the convergence study of DFT calculations can be found.
Supplementary Data for these DFT simulations of silica-water interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401050
Chapter 5: Kinetic Monte Carlo Model of Dynamic Surface Charging.
The folder "KMC": Contains input and output files for the Kinetic Monte Carlo simulations found in Chapter 5 of the thesis. Simulated using the Zacros version 1.01 software.
Chapter 6: Modelling the Net Charge of Proteins
The folder "modelling_net_charges" contains the pH titration results for TNF_alpha and Streptavidin calculated using MOE 2013.8 and PROPKA.
Chapter 7: Electrical Double Layer Dynamics at the Silica-Water Interface
Supplementary Data for these MD simulations of silica-water-biomolecules interactions can be found with the corresponding paper, or at doi:10.5258/SOTON/401018
Chapter 8: Quantitative Analysis of FET-Sensor Literature Data: From pH Sensing to Biosensing
The folder "streptavidin_meta_analysis" contains the summarised quantitative data used to plot the results. The plots were peformed using iPython and can be found in an iPython notebook file "streptavidin_notebook.ipynb"
"Surface Charge Calculations.ipynb" contains general calculations relating to estimating the surface charge density using the Poisson Boltzman equation (linearised vs non linearised). This was used to help choose the surface potential in the Gouy-Chapman-Stern model of Chapter 7.
The archive onetepconv.zip contains the OnetepConv software discussed in Chapter 4, and available online at: https://github.com/holyone2/onetepconv</span
Supplementary Data for Paper Entitled "Dynamic Behaviour of the Silica-Water-Bio Electric Double Layer in the Presence of Divalent Electrolyte"
No full textThis deposit includes supplementary data for the paper:
Lowe, B.M., Maekawa, Y., Shibuta, Y., Sakata, T., Skylaris, C.-K. and Green, N.G. (2016) Dynamic Behaviour of the Silica-Water-Bio Electrical Double Layer in the Presence of a Divalent Electrolyte. Physical Chemistry Chemical Physics, https://doi.org/10.1039/C6CP04101A
The data include:
- High-Resolution Molecular Dynamics Videos (.avi) "MD_video_trajectories.zip"
- Molecular Dynamics Trajectories (.xyz file format) "xyz_files.tar.bz2" [Now separated into 6 tar archives, all ending "_xyz_file.tar]
- Data files - Data extracted form the Trajectories, such as the charge distribution and water orientation "data.tar.bz2"
- Code used to analyse the data, and to plot the graphs in the publication - "analysis_and_images.zip"
Funded by JSPS 2015 Summer Fellowship.</span
Molecular dynamics simulation of potentiometric sensor response: Effect of biomolecules, surface morphology and surface charge
No full textThe silica-water interface is critical to many modern technologies in chemical engineering and biosensing. One technology used commonly in biosensors, the potentiometric sensor, operates by measuring changes in electric potential due to changes in the interfacial electric field. Predictive modelling of this response caused by surface binding of biomolecules remains highly challenging. In this work, through the most extensive molecular dynamics simulation of the silica-water interfacial potential and electric field to-date, we report novel prediction and explanation of the effects of nano-morphology on sensor response. Amorphous silica demonstrated a larger potentiometric response than an equivalent crystalline silica model due to increased sodium adsorption, in agreement with experiments showing improved sensor response with nano-texturing. We provide proof-of-concept that molecular dynamics can be used as a complementary tool for potentiometric biosensor response prediction. Effects that are conventionally neglected, such as surface morphology, water polarisation, biomolecule dynamics and finite-size effects are explicitly modelled
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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